+
Open data
-
Basic information
Entry | Database: PDB / ID: 4v6x | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the human 80S ribosome | |||||||||
![]() |
| |||||||||
![]() | RIBOSOME / eukarya / eukaryotic / ribosomal / 80S / RNA / protein synthesis / mass spectrometry | |||||||||
Function / homology | ![]() Synthesis of diphthamide-EEF2 / translation at postsynapse / cytoplasmic translational elongation / ribosome hibernation / translation elongation factor binding / PML body organization / response to folic acid / SUMO binding / translation at presynapse / exit from mitosis ...Synthesis of diphthamide-EEF2 / translation at postsynapse / cytoplasmic translational elongation / ribosome hibernation / translation elongation factor binding / PML body organization / response to folic acid / SUMO binding / translation at presynapse / exit from mitosis / eukaryotic 80S initiation complex / negative regulation of protein neddylation / response to insecticide / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / regulation of G1 to G0 transition / positive regulation of base-excision repair / axial mesoderm development / negative regulation of formation of translation preinitiation complex / positive regulation of cytoplasmic translation / regulation of translation involved in cellular response to UV / positive regulation of respiratory burst involved in inflammatory response / ribosomal protein import into nucleus / optic nerve development / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein-DNA complex disassembly / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinal ganglion cell axon guidance / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / GAIT complex / A band / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / supercoiled DNA binding / alpha-beta T cell differentiation / neural crest cell differentiation / G1 to G0 transition / positive regulation of ubiquitin-protein transferase activity / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / aggresome / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / middle ear morphogenesis / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / protein kinase A binding / Ribosomal scanning and start codon recognition / pigmentation / homeostatic process / lncRNA binding / response to aldosterone / Translation initiation complex formation / positive regulation of mitochondrial depolarization / Uptake and function of diphtheria toxin / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / lung morphogenesis / male meiosis I / positive regulation of activated T cell proliferation / monocyte chemotaxis / negative regulation of translational frameshifting / Protein hydroxylation / TOR signaling / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / iron-sulfur cluster binding / Peptide chain elongation / skeletal muscle cell differentiation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å | |||||||||
![]() | Anger, A.M. / Armache, J.-P. / Berninghausen, O. / Habeck, M. / Subklewe, M. / Wilson, D.N. / Beckmann, R. | |||||||||
![]() | ![]() Title: Structures of the human and Drosophila 80S ribosome. Authors: Andreas M Anger / Jean-Paul Armache / Otto Berninghausen / Michael Habeck / Marion Subklewe / Daniel N Wilson / Roland Beckmann / ![]() Abstract: Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex ...Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 5.4 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 578.5 KB | Display | |
Data in CIF | ![]() | 910.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5592MC ![]() 5591C ![]() 4v6wC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 3 types, 3 molecules AzAgAh
#1: Protein | Mass: 95463.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#35: Protein | Mass: 45051.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+40S ribosomal protein ... , 32 types, 32 molecules AUAKAOAXAMASAdANALARAPATABAAAVAYAZAaAbAcADAeAfAJAEACAGAFAHAWAIAQ
-RNA chain , 5 types, 5 molecules B2BCA5A7A8
#36: RNA chain | Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#37: RNA chain | Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#85: RNA chain | Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#86: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#87: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+60S ribosomal protein ... , 44 types, 44 molecules CzCKCOCLCVCMCaCNCICDCQCRCACSCTCPCUCXCYCWCZCrChCbCBCFCcCdCeCf...
-60S acidic ribosomal protein ... , 3 types, 5 molecules CqCsCtCuCv
#39: Protein | Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
---|---|---|---|
#83: Protein | Mass: 11521.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #84: Protein | Mass: 11676.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Details
Has protein modification | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: 80S human ribosome from PBMCs / Type: RIBOSOME |
---|---|
Molecular weight | Value: 4.5 MDa / Experimental value: NO |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % Details: Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV). |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS / Date: Feb 11, 2011 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 90000 X / Calibrated magnification: 90000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-
Processing
EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: each subvolume | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: Projection matching / Resolution: 5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 343343 / Nominal pixel size: 1.2375 Å / Actual pixel size: 1.2375 Å / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
|